Fitting EXAFS with out any atomic coordinates?
Hi Bruce my name is Mario and I was just wondering if your program can fir the EXAFS spectra without any atomic positions. Obviously the answer is no if you use atoms to create the FEFF file but what does one do when we have a semi-crystalline material for which no one has attempted the fractional coordinates. I mean the XRD pattern shows some crystalline but due to the high background I would think it would be very hard to do the Rietveld analysis. So what can one do, can we fit the EXAFS spectra knowing only the chemical composition and perhaps the lattice geometry(orthorhombic or hexagonal)? thanks
On Wednesday 28 March 2007 13:15, Mario Gomez wrote:
Hi Bruce my name is Mario and I was just wondering if your program can fir the EXAFS spectra without any atomic positions. Obviously the answer is no if you use atoms to create the FEFF file but what does one do when we have a semi-crystalline material for which no one has attempted the fractional coordinates.
I mean the XRD pattern shows some crystalline but due to the high background I would think it would be very hard to do the Rietveld analysis.
So what can one do, can we fit the EXAFS spectra knowing only the chemical composition and perhaps the lattice geometry(orthorhombic or hexagonal)?
Mario, Scott's answer was excellent, but I like the sound of my own voice so I thought I'd answer as well ;-) The Feff+Ifeffit+Artemis zeitgeist requires a list of atomic coordinates to begin analysis. Except in the rare situations, we don't know the actual arrangement of atoms. Indeed, to find out is one of the reasons we might do EXAFS. As Scott suggested, thinking about what you sample resembles is usually a good place to start. Consider amorphous germanium as an example. aGe is typically described as a continuous random network of bonds which are about the same length as the bonds in crystalline Ge. Because of that, crystalline Ge is a good place to start. In fact, I suspect that you could make considerable progress in analyzing aGe data with that one Feff calculation on the well-ordered material. EXAFS analysis is something of a creative endeavor -- the trick is to figure out how to use things that you know to model things that you don't know. Reading papers by the folks who answer questions on this list (Scott Calvin, Shelly Kelly, Anatoly Frenkel, Paul Fons) is a really good source of ideas for your own work with Ifeffit&Artemis. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/
Since I like the sound of my voice too, I will translate the "zeitgeist" from Bruce's email. According to Wikipedia, "It is originally a German expression that means "the spirit (Geist) of the time (Zeit)". Can it be loosely translate here as "poltergeist"? Anatoly -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: Wednesday, March 28, 2007 3:41 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates? On Wednesday 28 March 2007 13:15, Mario Gomez wrote:
Hi Bruce my name is Mario and I was just wondering if your program can fir the EXAFS spectra without any atomic positions. Obviously the answer is no if you use atoms to create the FEFF file but what does one do when we have a semi-crystalline material for which no one has attempted the fractional coordinates.
I mean the XRD pattern shows some crystalline but due to the high background I would think it would be very hard to do the Rietveld analysis.
So what can one do, can we fit the EXAFS spectra knowing only the chemical composition and perhaps the lattice geometry(orthorhombic or hexagonal)?
Mario, Scott's answer was excellent, but I like the sound of my own voice so I thought I'd answer as well ;-) The Feff+Ifeffit+Artemis zeitgeist requires a list of atomic coordinates to begin analysis. Except in the rare situations, we don't know the actual arrangement of atoms. Indeed, to find out is one of the reasons we might do EXAFS. As Scott suggested, thinking about what you sample resembles is usually a good place to start. Consider amorphous germanium as an example. aGe is typically described as a continuous random network of bonds which are about the same length as the bonds in crystalline Ge. Because of that, crystalline Ge is a good place to start. In fact, I suspect that you could make considerable progress in analyzing aGe data with that one Feff calculation on the well-ordered material. EXAFS analysis is something of a creative endeavor -- the trick is to figure out how to use things that you know to model things that you don't know. Reading papers by the folks who answer questions on this list (Scott Calvin, Shelly Kelly, Anatoly Frenkel, Paul Fons) is a really good source of ideas for your own work with Ifeffit&Artemis. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Anatoly,
it's funny for me as an german guy to read your discussion about "zeitgeist" and "poltergeist" ;-)
I think zeitgeist (the spirit of the time/age) and poltergeist are total different things.
Poltergeist:
maybe this is a good definition: Reports of poltergeist activity typically feature heavily on raps, bumps, thumps, knocks, footsteps, and bed-shaking, all without a discernible point of origin or physical reason for occurrence (http://en.wikipedia.org/wiki/Poltergeist). But if you look closer at it, you find out that it is a practical joke or nature phenomena like wind, wether etc... are the cause.
Ciao,
Eckhard
PS: sorry for the off-topic spam ;-)
-------- Original-Nachricht --------
Datum: Wed, 28 Mar 2007 16:43:35 -0400
Von: "Anatoly Frenkel"
Since I like the sound of my voice too, I will translate the "zeitgeist"
from Bruce's email. According to Wikipedia, "It is originally a German expression that means "the spirit (Geist) of the time (Zeit)". Can it be loosely translate here as "poltergeist"?
Anatoly -- "Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ... Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail
participants (4)
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Anatoly Frenkel
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Bruce Ravel
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E. Bosman
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Mario Gomez